Structure of PDB 6hko Chain B

Receptor sequence

>6hkoB (length=1166) Species: 559292 (Saccharomyces cerevisiae S288C)

ARTADFRTLERESRFINPPKDKSAFPLLQEAVQPHIGSFNALTEGPDGGL
LNLGVKDIGEKVIFDGKPGYLGNKLSVSVEQVSIAKPMSNDAVERKVYPS
ESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQSNRCHLNK
MSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFAN
RGASYSHYGIQIRSVRPDQTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVV
MILKALCHTSDREIFDGIIGNDVKDSFLTDRLELLLRGFKKRYPHLQNRT
QVLQYLGDKFRVVFQASPDQSDLEVGQEVLDRIVLVHLGKDGSQDKFRML
LFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNI
IAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQYFLSTGNLVSQS
GLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTTVRKLLPES
WGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSILYSLGVAPAS
HTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADTLRYWKVEGKTPGLPIDL
EIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKEDIVGPFEQVYMNI
AVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQ
TMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVA
VISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITQH
FGFGNDEWPKEWLEKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTY
HSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGDKFSSRHGQK
GVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGAL
HGIAQDSTPWIFNEDDTPADYFGEQLAKAGYNYHGNEPMYSGATGEELRA
DIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEM
ERDALIGHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQSVPRIGSIS
TVCCRRCSMRFEDAKIDDSQIWEDGQGNKFVGGNETTTVAIPFVLKYLDS
ELSAMGIRLRYNVEPK

3D structure

• PDB: 6hko The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2.
• Chain: B
• Resolution: 3.42 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	B	S482 V486 R495 Q720 Q724 K916 K924 H1038 R1065	S458 V462 R471 Q696 Q700 K892 K900 H1014 R1041
BS02	dna	B	R219 S221 Q479 F508 R817	R195 S197 Q455 F484 R793
BS03	dna	B	N197 M430 N454 Y463 S466 N739 Q1045 G1062 R1063 R1070 M1074	N173 M406 N430 Y439 S442 N715 Q1021 G1038 R1039 R1046 M1050
BS04	ZN	B	C1107 C1131	C1083 C1107
BS05	G2P	B	R714 R957	R690 R933

Gene Ontology

Molecular Function

• GO:0001054 RNA polymerase I activity
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0032549 ribonucleoside binding
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0006360 transcription by RNA polymerase I
• GO:0006361 transcription initiation at RNA polymerase I promoter
• GO:0006362 transcription elongation by RNA polymerase I
• GO:0006363 termination of RNA polymerase I transcription
• GO:0042254 ribosome biogenesis
• GO:0042790 nucleolar large rRNA transcription by RNA polymerase I

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005736 RNA polymerase I complex

External links

• PDB: RCSB:6hko, PDBe:6hko, PDBj:6hko
• PDBsum: 6hko
• PubMed: 30913026
• UniProt: P22138|RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135 (Gene Name=RPA135)